These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
In the anime, Misaki is either just a depressed girl looking for affection and purpose, or she's a broken and manipulative stalker that's trying to force a shut-in to spend time/be in a relationship with her. It all depends on your point of view.
Also in the anime, Satou is either someone who is just not sure what to do with their life, or one of the most selfish people in the series who constantly scolds others for trying to help him.
Manga Satou is worse. At least anime Satou attempts to improve (especially having his food supply get cut off).
And isn't Hitomi ultimately the one who messed up Satou's head with her terminal nihilism and constant rambling about conspiracies? One might think she secretly enjoys the power she has over him.
Overlaps with the Misaimed Fandom for a lot of readers. Even if it's better to deal with life head-on, looking at a character who for a lot of otaku with anxiety problems is like a disturbingly reflective mirror, it just becomes painful to read and causes them to become even bigger introverts. An understandable choice, as even the author succumbed to it.
Idiot Plot: The pyramid scheme (sorry, "Multi-Level Marketing") storyline in the anime. The characters genuinely believe in the scams for long enough, but it's Played for Laughs.
It's not so straightforward: Satou suspects it from the start and doesn't need to see much evidence to convince him. Yet while Megumi was genuinely suckered in, she gets Satou because she tells him it's a scam, that he can use to 'take revenge' on the world. Misaki is taken by Megumi, believe it or not, trying to get back Satou's money. Megumi's pretty good at this.
Iron Woobie: While Yamazaki may not seem like an obvious woobie because he doesn't complain about his problems, he was bullied in school, left home because his parents tried to plan out every detail of his future, designed a game that failed spectacularly, and eventually had to give up his dreams and move back to the life he was trying to escape.
Keep Circulating the Books: The manga and light novel were licensed by Tokyopop. The manga sold reasonably well, but fell out of print after TP shut down, was not rescued by anyone, and volumes are increasingly difficult to find even on the used market. The novel had only a small print run, and tends to command a ridiculously high price on the rare occasion it appears on retail/auction sites.
The anime, by contrast, is much easier to find, especially if you're in the USA, since Funimation uploaded the entire thing onto its website (and for non-Americans there are... other methods).
Misaimed Fandom: Introverted fans of the series can often be found wishing they knew someone like Misaki in their life, despite the series' message that this comes with its own set of problems.
It's better than knowing no girls.
Not to mention they ultimately still benefited from their creepy little relationship.
An alternate interpretation is that selflessly devoting oneself to another can be harmful, whereas mutual assistance can save all involved.
Misaki's portrayal in the novel and anime is a bit easier to swallow. Her personality issues in the manga are quite a bit more frightening.
The amount of people who have watched or read this series and still proudly declare themselves as a Hikikomori on the Internet - yes, including This Very Wiki - is staggering and depressing.
Finally getting a diagnosis can be a huge relief. Being able to put a name on the problem is a first step towards fixing it. Or it can let someone write off their personality defects as symptoms of something they can't help rather than putting the hammer down and actually sorting their life out.
There are people taking Yamazaki's misogyny as gospel. While his betrayal by women in his life can be seen in sympathetic light, the whole point of his misogyny is that it's the wrong way to react.
In particular, the first hints of what happened to Misaki are stomach-churning.
And the episode where Yamazaki moves back to his farm realizing that his dream is futile. Hell, all of the last 4 episodes qualify.
The Woobie: Satou. He's a good person, he just doesn't know it. Misaki also qualifies once you learn why she wants to help Satou: her mother committed suicide, she blames herself and considers herself to be worthless and wants to find a friend/lover who's more pathetic than her.
Jerkass Woobie - Megumi. While she scammed a lot of people, she did it to support her older hikikomori brother, who she cared about a lot. She doesn't exactly seem proud of her actions either.
Her brother also qualifies, once he stops being a hikikomori and puts the moves on Misaki because Satou didn't/couldn't.